Query 027008
Match_columns 229
No_of_seqs 53 out of 55
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 03:40:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027008.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027008hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08536 Whirly: Whirly transc 100.0 4.5E-71 9.8E-76 455.3 14.9 139 90-228 1-139 (139)
2 PF02035 Coagulin: Coagulin; 66.1 6 0.00013 34.3 2.9 51 85-142 75-125 (174)
3 PRK12301 bssS biofilm formatio 62.1 2.4 5.2E-05 33.5 -0.2 16 1-16 27-42 (84)
4 PF13991 BssS: BssS protein fa 29.4 26 0.00055 27.0 0.8 16 1-16 17-32 (73)
5 PF10657 RC-P840_PscD: Photosy 21.5 63 0.0014 27.7 1.8 20 116-135 40-59 (144)
6 PRK04179 rpl37e 50S ribosomal 19.8 32 0.00069 25.9 -0.2 14 129-142 42-55 (62)
7 PF07490 Tir_receptor_N: Trans 17.9 1.7E+02 0.0036 27.2 3.8 60 160-226 85-145 (266)
8 PF01907 Ribosomal_L37e: Ribos 17.2 60 0.0013 23.9 0.7 13 129-141 39-52 (55)
9 PF11807 DUF3328: Domain of un 15.0 48 0.001 26.6 -0.3 11 1-11 127-137 (217)
10 PF13103 TonB_2: TonB C termin 14.6 91 0.002 22.2 1.1 25 115-139 32-57 (85)
No 1
>PF08536 Whirly: Whirly transcription factor; InterPro: IPR013742 This is a family of plant transcription factors. ; PDB: 3R9Y_A 3N1I_A 3N1K_A 3RA0_A 3N1H_A 3N1J_A 3N1L_A 3R9Z_A 1L3A_D.
Probab=100.00 E-value=4.5e-71 Score=455.34 Aligned_cols=139 Identities=74% Similarity=1.128 Sum_probs=123.9
Q ss_pred eeeeCceeEEEeecCCceeecCCcceEEeeeceEEEEeecccccccccCccceEEeeehhhhhhhhhcCccccceeeecC
Q 027008 90 SIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDP 169 (229)
Q Consensus 90 sIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPA~G~RqYDW~kKq~FsLS~tEvG~LisLg~~~s~efFHDP 169 (229)
+||||||||+|+|++|+|++++||+++++|+|+||||||||+|+|||||+|||+|+|||+|+|+||+|+++++|||||||
T Consensus 1 sVYk~kaAl~v~p~~P~f~~~~sg~~kv~R~G~vlLefapa~g~r~YDW~kKq~FsLS~tEvG~ll~l~~~~s~effHdP 80 (139)
T PF08536_consen 1 SVYKGKAALSVRPIKPTFTSLDSGYFKVSREGSVLLEFAPAVGPRQYDWSKKQTFSLSPTEVGSLLSLGARESCEFFHDP 80 (139)
T ss_dssp EEEESSEEEEEEEE--EEEE-TTSCEEEEC--EEEEEEEEBCSTTEB-GGG-EEEEE-HHHHHHHHT--TT--EEEEE-T
T ss_pred CccccceeEEEEecCCccEECCCCcEEEeeccEEEEEEccccCCcccccccceEEEEcHHHhhhhhhhccCCceEEEecc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCceeEEEEEEeCCCCCcceEEEEeeeccccCCcceeeeechhhHHHHhhhhc
Q 027008 170 FKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228 (229)
Q Consensus 170 ~~g~S~~G~vrK~LkVeP~pDgSG~ffnLsV~n~~~n~de~~~iPVt~aEfaVl~S~f~ 228 (229)
+||+|++|+|||+|||||+|||+|+||||+|+|++.|++++|+||||+|||||||++||
T Consensus 81 ~~~~s~~G~v~K~Lkv~p~~dgsg~f~~Lsv~~~~~~~~~~~~ipVt~aEfavl~s~f~ 139 (139)
T PF08536_consen 81 NMGSSNEGKVRKSLKVEPLPDGSGYFFNLSVQNKLLNGDENFSIPVTKAEFAVLRSAFN 139 (139)
T ss_dssp TTTSTTTTSEEEEEEEEE-TTSSEEEEEEEEEECCCTEEEEEEEEEEHHHHHHHHHHHH
T ss_pred ccCCCCCCceEEEEEeEECCCCCceEEEEEEecccccccceEEEechHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999999999996
No 2
>PF02035 Coagulin: Coagulin; InterPro: IPR000275 Coagulogen is a gel-forming protein of hemolymph that hinders the spread of invaders by immobilising them [, ]. The protein contains a single 175- residue polypeptide chain; this is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). Cleavage releases two chains of coagulin, A and B, linked by two disulphide bonds, together with the peptide C [, ]. Gel formation results from interlinking of coagulin molecules. Secondary structure prediction suggests the C peptide forms an alpha- helix, which is released during the proteolytic conversion of coagulogen to coagulin gel []. The beta-sheet structure and 16 half-cystines found in the molecule appear to yield a compact protein stable to acid and heat. Mammalian blood coagulation is based on the proteolytically induced polymerisation of fibrinogens. Initially, fibrin monomers noncovalently interact with each other. The resulting homopolymers are further stabilised when the plasma transglutaminase (TGase) intermolecularly cross-links epsilon-(gamma-glutamyl)lysine bonds. In crustaceans, hemolymph coagulation depends on the TGase-mediated cross-linking of specific plasma-clotting proteins, but without the proteolytic cascade. In horseshoe crabs, the proteolytic coagulation cascade triggered by lipopolysaccharides and beta-1,3-glucans leads to the conversion of coagulogen into coagulin, resulting in noncovalent coagulin homopolymers through head-to-tail interaction. Horseshoe crab TGase, however, does not cross-link coagulins intermolecularly. Recently, we found that coagulins are cross-linked on hemocyte cell surface proteins called proxins. This indicates that a cross-linking reaction at the final stage of hemolymph coagulation is an important innate immune system of horseshoe crabs [].; GO: 0042381 hemolymph coagulation, 0005576 extracellular region; PDB: 1AOC_A.
Probab=66.15 E-value=6 Score=34.29 Aligned_cols=51 Identities=24% Similarity=0.395 Sum_probs=27.0
Q ss_pred eeeeeeeeeCceeEEEeecCCceeecCCcceEEeeeceEEEEeecccccccccCccce
Q 027008 85 VYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQ 142 (229)
Q Consensus 85 Vy~~ysIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPA~G~RqYDW~kKq 142 (229)
-|.+|.-|+...-.+.+..-|.|.---+|.+++ +-=||.+|-||--|+.|-
T Consensus 75 nf~pf~hf~secpvstrdcepvfgyt~a~efrv-------ivqapragfrqcvwqhkc 125 (174)
T PF02035_consen 75 NFPPFHHFKSECPVSTRDCEPVFGYTVAGEFRV-------IVQAPRAGFRQCVWQHKC 125 (174)
T ss_dssp GSTT----SSB--EEEE----SEEE-TTS-EEE-------E--BCCCTB-B---EEEE
T ss_pred cCCCcccccccCCcccccccccccceecceEEE-------EEeCchhhHHHHHHHhhh
Confidence 356788899999999999999998877777654 345899999999999884
No 3
>PRK12301 bssS biofilm formation regulatory protein BssS; Reviewed
Probab=62.13 E-value=2.4 Score=33.51 Aligned_cols=16 Identities=31% Similarity=0.565 Sum_probs=13.7
Q ss_pred CceeeeeccccCCCCC
Q 027008 1 MMLQLQCLSSQTLNPK 16 (229)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (229)
||++||.|||+.|.+.
T Consensus 27 mmirlhyLss~~Q~~e 42 (84)
T PRK12301 27 LMLRLHYQSPNDQEPE 42 (84)
T ss_pred HHHhhhhcCCCCCCcc
Confidence 7999999999977653
No 4
>PF13991 BssS: BssS protein family
Probab=29.37 E-value=26 Score=27.02 Aligned_cols=16 Identities=44% Similarity=0.663 Sum_probs=13.3
Q ss_pred CceeeeeccccCCCCC
Q 027008 1 MMLQLQCLSSQTLNPK 16 (229)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (229)
||++||.|+++.|.+.
T Consensus 17 l~lrl~yls~~~q~~e 32 (73)
T PF13991_consen 17 LMLRLHYLSSPDQPPE 32 (73)
T ss_pred eEEEecccCCCCCCcc
Confidence 7999999999977643
No 5
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=21.46 E-value=63 Score=27.71 Aligned_cols=20 Identities=40% Similarity=0.594 Sum_probs=18.7
Q ss_pred EEeeeceEEEEeeccccccc
Q 027008 116 KLSREGFVMLQFAPAAGVRQ 135 (229)
Q Consensus 116 kv~R~G~vlLeFAPA~G~Rq 135 (229)
|.+|.|.+=||++||.|-|+
T Consensus 40 kRD~~g~Lql~i~pasGrrk 59 (144)
T PF10657_consen 40 KRDRYGKLQLTISPASGRRK 59 (144)
T ss_pred ecccCCceEEEEecCCCccc
Confidence 78999999999999999886
No 6
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=19.79 E-value=32 Score=25.92 Aligned_cols=14 Identities=29% Similarity=0.852 Sum_probs=10.5
Q ss_pred cccccccccCccce
Q 027008 129 PAAGVRQYDWSRKQ 142 (229)
Q Consensus 129 PA~G~RqYDW~kKq 142 (229)
|+.--|.|+|+.|-
T Consensus 42 ps~k~R~YnWs~Ka 55 (62)
T PRK04179 42 RSKRIRRYSWQNKK 55 (62)
T ss_pred cccccccccHHHHh
Confidence 45556999999874
No 7
>PF07490 Tir_receptor_N: Translocated intimin receptor (Tir) N-terminus; InterPro: IPR022633 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia []. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason []. Enteropathogenic and entero- haemorrhagic Escherichia coli secrete the bacterial adhesion mediation molecule intimin [], which targets the translocated intimin receptor, Tir. Tir is secreted by the bacteria and is embedded in the target cell's plasma membrane []. This facilitates bacterial cell attachment to the host.
Probab=17.88 E-value=1.7e+02 Score=27.23 Aligned_cols=60 Identities=20% Similarity=0.242 Sum_probs=40.9
Q ss_pred cccceeeecCCCCCCC-CCceeEEEEEEeCCCCCcceEEEEeeeccccCCcceeeeechhhHHHHhhh
Q 027008 160 RESCEFFHDPFKGKSE-EGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSA 226 (229)
Q Consensus 160 ~~s~efFHDP~~g~S~-~G~vrK~LkVeP~pDgSG~ffnLsV~n~~~n~de~~~iPVt~aEfaVl~S~ 226 (229)
.+++|..||-.-...- ..-=.-+|.||-.+||+ ..-+..+|.+ ..+|-++..||+-|+++
T Consensus 85 ~ggfEVLHD~G~LDtLN~~IGss~FrvE~q~dG~--h~AiGqk~gv-----EtsV~Ls~qE~~sLQai 145 (266)
T PF07490_consen 85 HGGFEVLHDKGPLDTLNKQIGSSVFRVETQEDGS--HVAIGQKNGV-----ETSVTLSEQELASLQAI 145 (266)
T ss_pred ccceEEeeccCchhhHHhhhCccceEEEeccCCc--eEeeeccCCe-----EEEEEeCHHHhhhhhcc
Confidence 4579999995443211 11123579999999984 4566555444 36889999999999875
No 8
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=17.25 E-value=60 Score=23.93 Aligned_cols=13 Identities=62% Similarity=1.147 Sum_probs=6.8
Q ss_pred cccccc-cccCccc
Q 027008 129 PAAGVR-QYDWSRK 141 (229)
Q Consensus 129 PA~G~R-qYDW~kK 141 (229)
|+.--| +|+|+.|
T Consensus 39 p~~kkrr~ynWs~K 52 (55)
T PF01907_consen 39 PAAKKRRKYNWSAK 52 (55)
T ss_dssp TTSSS----SSSSH
T ss_pred Ccccccccccchhh
Confidence 444456 9999987
No 9
>PF11807 DUF3328: Domain of unknown function (DUF3328); InterPro: IPR021765 This family of proteins are functionally uncharacterised. This family is only found in eukaryotes.
Probab=14.99 E-value=48 Score=26.61 Aligned_cols=11 Identities=36% Similarity=0.685 Sum_probs=8.0
Q ss_pred Cceeeeecccc
Q 027008 1 MMLQLQCLSSQ 11 (229)
Q Consensus 1 ~~~~~~~~~~~ 11 (229)
|+||||||..-
T Consensus 127 vfHqLHCL~~l 137 (217)
T PF11807_consen 127 VFHQLHCLNML 137 (217)
T ss_pred cchhhhhhHHH
Confidence 57889998543
No 10
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=14.56 E-value=91 Score=22.21 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=17.7
Q ss_pred eEEeeeceE-EEEeecccccccccCc
Q 027008 115 VKLSREGFV-MLQFAPAAGVRQYDWS 139 (229)
Q Consensus 115 ~kv~R~G~v-lLeFAPA~G~RqYDW~ 139 (229)
++++++|.| -.++....|...||-.
T Consensus 32 i~i~~dG~v~~~~i~~sSG~~~~D~a 57 (85)
T PF13103_consen 32 ITIDPDGRVISVRIVKSSGNPAFDAA 57 (85)
T ss_dssp EEE-TTSBEEEEEEEE--S-HHHHHH
T ss_pred EEECCCCCEEEEEEecCCCCHHHHHH
Confidence 578999998 7888899999999965
Done!